[gmx-users] crystals of KCl during simulation

Marc Baaden baaden at smplinux.de
Mon Jun 1 14:34:55 CEST 2009


regafan at hotmail.com said:
>> [..] but after equilibration I have observed that KCl is aggregating, like
>> if it was making crystals. When I used NaCl instead KCl, this not
>> happened.

>> Does anybody has any idea about the reason of the behaviour of KCl in
>> the simulation?

This even does happen with Amber :)  So my guess is you correctly transferred
the parameters, but stumbled upon an artefact. If you check the recent 
literature you may notice that many publications with Amber using K+ 
only employ minimal (neutralising) salt conditions as a workaround. At 
least this is what we did recently [1].

Marc Baaden

[1] Interactions between neuronal fusion proteins explored by molecular
dynamics, Biophys.J.94, 2008, 3436-3446.

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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